An unholy war has erupted over stained-glass windows that disappeared from a shuttered Bronx synagogue recently purchased by the Catholic Church.

The windows – depicting the Star of David and bearing the names of members of the former Mosholu Jewish Center on Hull Avenue – vanished during renovations of the temple, which is being converted into a Head Start facility by the New York Archdiocese.

“An important and sacred legacy of a 70-year- old synagogue has disappeared, and nobody seems to be accountable for what happened to them,” said Dr. Charles Bierman, who was on the committee that shepherded its 1999-2000 sale to the archdiocese. Bierman said he hoped the windows would be given to another synagogue or Jewish institution.

Bierman claims archdiocese officials reneged on a deal that would have let him have the windows.

The archdiocese counters that Bierman is a troublemaker who didn’t hold up his end of the bargain regarding removal of the windows, and now it’s too late.

“The windows no longer exist,” said archdiocese spokesman Joe Zwilling. Asked whether the archdiocese felt it had an ethical obligation to preserve the windows, Zwilling referred calls to David Pollock and Marcia Eisenberg, executives of the Jewish Community Relations Council.

JCRC, a group founded to “protect and defend Jewish interests,” helped broker the synagogue sale to the church.

“I’d imagine if they had felt this was important to them, they would have dealt with it,” Zwilling said.

Pollock didn’t return repeated calls. Eisenberg was on vacation.

Meanwhile, nobody seems to know exactly what happened to the windows.

Bierman said he was told the windows “fell apart” when they were removed.

A construction source told The Post the windows were removed intact.

Nora Fuery, who runs the Head Start program and oversees the renovation, said: “I don’t know anything about any windows.”

She also denied knowledge of a letter from an archdiocese lawyer to Pollock and herself outlining a deal in which Bierman would be allowed to take the windows if he paid for removal and replacement. Bierman said: “When renovation started . . . they refused to make good on their promise.”

Countered Zwilling: “Dr. Bierman was given ample opportunity – which he never followed up on – to have the windows removed.”

In April 2001, Bierman was booted from involvement with the deal by synagogue officials, who found he was “acting inappropriately.”

“This is a case of one guy trying to create a fight between the archdiocese and the Jewish community where one doesn’t exist,” said Zwilling.

Bierman said, “I’m not a troublemaker, I’m persistent – I tried to hold them to what they promised.”